I'm unsure how to mark it. I'm not ready to say it is off-topic, because it sort of works on both sites, but the flagging tool doesn't allow me to mark something as a duplicate against another StackExchange site.

2 Answers
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There is no notion of cross-site duplicates. If the questions are on-topic on both sites, both should be retained. Please link to the other question in a comment or answer on each side, so that askers, potential answerers and future visitors know where to find the work that already exists on the subject. The idea behind keeping both versions is that the questions are reaching two different communities and may receive different answers. If you've answered on one side and your answer would be appropriate on the other side and doesn't duplicate an existing answer, feel free to repost it on the other side (adapting to the different community if necessary).

Of course, if the question is off-topic on one site, it should be closed as off-topic.

If the two questions are identical and posted by the same user at the same time, this is a cross-post (or more precisely a multi-post), and these are strongly discouraged. Here the reason is that asking two identical questions duplicates efforts on the answerers' part.

They have turned down the request to allow closing as dupes between sites (though I'm not sure I'd do that in this case anyway, since the SO question might end up with some programming answers). What you did by putting a comment on there linking to the other question is the appropriate response.